Hi Adrian and Dan,
I just tried the A9 tutorial again and can confirm that it takes way to
long (ParmEd from Amber16). But I have checked also with the old
version from Amber 14 and it only took about 1 minute.
Cheers,
Hannes.
On Thu, 16 Mar 2017 15:47:31 -0700
Daniel Mermelstein <danmermelstein35.gmail.com> wrote:
> Hi Adrian,
>
> I have one VERY ROUGH data point: I merged two copies of a 4300 atom
> protein, and it took about a week. I don't know exactly how long
> because I forgot it was still running...I also know an undergrad
> working for me tried to run the sidechain timerge tutorial and gave
> up after a couple days, in case that's useful
>
> Dan
>
> On Thu, Mar 16, 2017 at 7:48 AM, Adrian Roitberg <roitberg.ufl.edu>
> wrote:
>
> > Dear all
> >
> > We are having trouble using the timerge function in parmed.
> >
> > In particular, if we try to follow the tutorials A9 for a change in
> > side chain, the system hangs for a long time.
> >
> > We are testing some smaller systems, and it seems that the scaling
> > with system size is really bad.
> >
> > Can someone give us some idea abou how long one might expect the
> > timerge to take vs system size ?
> >
> > thanks
> >
> > adrian
> >
> >
> >
> > --
> > Dr. Adrian E. Roitberg
> > University of Florida Research Foundation Professor.
> > Department of Chemistry
> > University of Florida
> > roitberg.ufl.edu
> > 352-392-6972
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Mar 17 2017 - 03:00:02 PDT
